Abstract: Disclosed are methods for the detection of loss of genomic integrity characteristic of genomic instability. The methods are especially useful for detection of deletions of genomic DNA that occur in early stages of Cancer, especially colorectal cancer. Methods of the invention involve the detection in a biological sample of a nucleic acid fragment which includes both 3' and 5' DNA sequence which normally flank a region where a deletion is suspected. The assay is designed as disclosed herein such that there is only a small or negligible likelihood that the fragment will be present unless a deletion has occurred.